How to seperate clothing from the rest of the model
There are two fundamental principles to 3D modeling. One is "don't model what can't be seen"; the other is "any part which needs to move independently of any other part needs to be a separate object  from every other part to which it moves in relation". Following these principles, your character will consist of multiple objects: a head, a separate jaw, likely separate eyes, a cap, a pair of hands, a pair of arms, a pair of feet, a pair of legs, and two or more objects  which, combined, make up the torso. 

In fact, you will likely have multiple feet: perhaps a pair of combat boots, a pair of parade dress, and a pair of ghillie boots. You won't usually have bot bare feet and shod feet, because you can't usually see the feet through the shoes.